That much is already obvious. The issue is how does one progress to the next level without being shown these things or told what one should be looking for?

It is naive to think that the teacher will show/tell you how to get to the next level in due course. One could waste years of valuable training barking up the wrong tree, even under "expert" supervision. It is also in my experience, that senior teachers within the art, do not seem to have specific knowledge of these aspects. Even if they do have specific knowledge, it is not something that they would readily share, despite the fact that these things are easily demonstrable. In many cases, they simply wave it off as "rubbish", akin to the pseudo-religious "nonsense" and "mumbo-jumbo" spouted by the Founder, which many in the art do not believe in.

Irregardless, my interest at this stage is purely research, specifically the similarities of specific finger and hand positioning, and the internal exercises between systems that appear to share this knowledge. I'm not particularly interested in how this is done, since I already have an idea of the connections via corroboration with TCM principles.

My hypothesis at this stage, is that the Founder was privy to very specific qigong knowledge via various Buddhist classics (some sources suggesting that this knowledge was widely recorded in the kojiki).

One of my unanswered questions at this stage is how ninjutsu came to possess this knowledge as well, and what is the source of that knowledge. I was hoping that someone who does ninjutsu could enlighten me. Specifically, what is the historical connection (if any) between the kuji-in as practiced by certain ninjutsu-ryu and tantric-yoga? Or was this knowledge handed down via Buddhist influences and how (i.e. thru whom)?

My knowledge of ninjutsu's historical development and roots is somewhat vague (since most of it seems to be clouded in myth and mystery - for obvious reasons). I'm just trying to sort out the facts from the myth.